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BCB
2010
213views Bioinformatics» more  BCB 2010»
13 years 2 months ago
Markov clustering of protein interaction networks with improved balance and scalability
Markov Clustering (MCL) is a popular algorithm for clustering networks in bioinformatics such as protein-protein interaction networks and protein similarity networks. An important...
Venu Satuluri, Srinivasan Parthasarathy, Duygu Uca...
JCC
2007
131views more  JCC 2007»
13 years 7 months ago
An extended dead-end elimination algorithm to determine gap-free lists of low energy states
: Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified...
Edda Kloppmann, G. Matthias Ullmann, Torsten Becke...
BMCBI
2010
156views more  BMCBI 2010»
13 years 7 months ago
Mathematical model for empirically optimizing large scale production of soluble protein domains
Background: Efficient dissection of large proteins into their structural domains is critical for high throughput proteome analysis. So far, no study has focused on mathematically ...
Eisuke Chikayama, Atsushi Kurotani, Takanori Tanak...
BMCBI
2007
160views more  BMCBI 2007»
13 years 7 months ago
Convergent algorithms for protein structural alignment
Background: Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually...
Leandro Martínez, Roberto Andreani, Jos&eac...
BMCBI
2008
133views more  BMCBI 2008»
13 years 7 months ago
LocateP: Genome-scale subcellular-location predictor for bacterial proteins
Background: In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phob...
Miaomiao Zhou, Jos Boekhorst, Christof Francke, Ro...